.TH g_potential 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_potential - calculates the electrostatic potential across the box

.B VERSION 4.5
.SH SYNOPSIS
\f3g_potential\fP
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-s" " topol.tpr "
.BI "\-o" " potential.xvg "
.BI "\-oc" " charge.xvg "
.BI "\-of" " field.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-d" " string "
.BI "\-sl" " int "
.BI "\-cb" " int "
.BI "\-ce" " int "
.BI "\-tz" " real "
.BI "\-[no]spherical" ""
.BI "\-ng" " int "
.BI "\-[no]correct" ""
.SH DESCRIPTION
\&Compute the electrostatical potential across the box. The potential is
\&calculated by first summing the charges per slice and then integrating
\&twice of this charge distribution. Periodic boundaries are not taken
\&into account. Reference of potential is taken to be the left side of
\&the box. It's also possible to calculate the potential in spherical
\&coordinates as function of r by calculating a charge distribution in
\&spherical slices and twice integrating them. epsilon_r is taken as 1,
\&2 is more appropriate in many cases.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input
 Index file 

.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-o" " potential.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-oc" " charge.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-of" " field.xvg" 
.B Output
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-d"  " string" " Z" 
 Take the normal on the membrane in direction X, Y or Z.

.BI "\-sl"  " int" " 10" 
 Calculate potential as function of boxlength, dividing the box in nr slices.

.BI "\-cb"  " int" " 0" 
 Discard first nr slices of box for integration

.BI "\-ce"  " int" " 0" 
 Discard last nr slices of box for integration

.BI "\-tz"  " real" " 0     " 
 Translate all coordinates distance in the direction of the box

.BI "\-[no]spherical"  "no    "
 Calculate spherical thingie

.BI "\-ng"  " int" " 1" 
 Number of groups to consider

.BI "\-[no]correct"  "no    "
 Assume net zero charge of groups to improve accuracy

.SH KNOWN PROBLEMS
\- Discarding slices for integration should not be necessary.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
